Custom web publishing would allow for you to do this as well, without far less licensing restrictions than WebDirect has.
Since your front-facing web does not really need the full "filemaker experience", just a place to upload files, WebDirect may not be the right choice.
However, using CWP does come with additional development needs (mainly, knowing PHP well enough to get by, and sometimes having a separate web host for your PHP code).
I had a similar problem. That I solved in a way similar to Mikes suggestion. In my case, we had the web developer use an open source solution (PHP/MySQL) for the customer portal. Then we used ESS to pull the data into FileMaker.
Your issue involves Container fields, so there will be some extra issues to deal with, but this might be a good avenue to explore.